Abstract
The t(14;18) translocation involving the Ig heavy chain locus and the BCL-2 gene is the single most common chromosomal translocation in human cancer. Recently we reported in vitro and in vivo chemical probing data indicating that the 150-bp major breakpoint region (Mbr), which contains three breakage subregions (hotspots) (known as peaks I, II, and III), has single-stranded character and hence a non-B DNA conformation. Although we could document the non-B DNA structure formation at the bcl-2 Mbr, the structural studies were limited to chemical probing. Therefore, in the present study, we used multiple methods including circular dichroism to detect the non-B DNA at the bcl-2 Mbr. We established a new gel shift method to detect the altered structure at neutral pH on shorter DNA fragments containing the bcl-2 Mbr and analyzed the fine structural features. We found that the single-stranded region in the non-B DNA structure observed is stable for days and is asymmetric with respect to the Watson and Crick strands. It could be detected by oligomer probing, a bisulfite modification assay, or a P1 nuclease assay. We provide evidence that two different non-B conformations exist at peak I in addition to the single one observed at peak III. Finally we used mutagenesis and base analogue incorporation to show that the non-B DNA structure formation requires Hoogsteen pairing. These findings place major constraints on the location and nature of the non-B conformations assumed at peaks I and III of the bcl-2 Mbr.
Highlights
The t(14;18) translocation is the most common translocation in human cancer
In the present study we showed that the bcl-2 major breakpoint region (Mbr) adopts a non-B DNA conformation at neutral pH that is sufficiently stable to discern by gel electrophoresis
We conclude that the structure requires Hoogsteen hydrogen bonding, and we can begin to consider the types of possible non-B DNA conformations that form at the bcl-2 Mbr
Summary
Major breakpoint region; ss, single-stranded; nt, nucleotide(s). the 3Ј untranslated region of the BCL-2 gene (3, 5, 10 –13). Major breakpoint region; ss, single-stranded; nt, nucleotide(s). We were able to reproduce the single-stranded character of the bcl-2 Mbr on human minichromosomes, indicating that this distinctive property does not rely on the sequence of the surrounding DNA. We were able to reproduce the single-stranded character when the Mbr was carried on prokaryotic plasmids (replicated in Escherichia coli), indicating that eukaryotic proteins are not necessary to generate the altered DNA structure. We used single-stranded DNA oligonucleotides to probe which regions of the structure are available for hydrogen bonding, and these probings provided an independent demonstration of the asymmetry in single-strandedness between the top and bottom strands. We conclude that the structure requires Hoogsteen hydrogen bonding, and we can begin to consider the types of possible non-B DNA conformations that form at the bcl-2 Mbr
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